In silico modeling

In this research paper we report the detailed synthesis, spectral (1H-NMR, FT-IR, and UV-Vis), crystal structure determination, DFT studies, and molecular modeling of 4-amino-3-mercapto-5-methyl-1,2,4-triazole (L2) Schiff base ligand and its complexes of cadmium as suitable bioactive agents for the treatment of malaria. From the spectroscopic results, the synthesized Schiff base has potentialtridentate coordination with themetal ion via hydroxy naphthalinic-O, azomethine-N and sulphur atom of the thione group.

17p dianmotminh02 03-05-2024 2 1   Download

This modeling is performed on an experimental data set of complexes, where the metal ions of these complexes include transition ion metals and lanthanide ion metals. We use these models to develop a series of new thiosemicarbazone and their complexes; simultaneously, the complexes are worked out the stability constants from the novel models.

9p dianmotminh02 03-05-2024 4 1   Download

Ebook "In silico modeling and experimental validation for improving methanogenesis from CO2 via M. maripaludis" explores the ability of M. maripaludis to capture and convert CO2 to methane in the presence of free nitrogen, and offers a consolidated review of the metabolic processes and applications of M. maripaludis. Further, it develops, validates and analyzes the first genome-scale metabolic model (iMM518) of M. maripaludis. Readers will discover, for the first time, the impact of nitrogen fixation on methane production.

140p tracanhphuonghoa1007 22-04-2024 4 2   Download

In ebook "Prion proteins (Topics in current chemistry, Volume 305)" we have assembled a set of chapters highlighting various aspects of prion diseases in humans and animals which show the intriguing features of both physiological and pathogenic PrP conformers. In addition, a wide spectrum of methodological approaches are described, ranging from in silico, chemical, and in vitro approaches to animal models, to illustrate the elaborate and extensive technology established in the prion field, allowing the analysis of disease mechanisms and the development of diagnostic and therapeutic strategies.

308p manmanthanhla0201 26-02-2024 11 1   Download

Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies.

24p vinarcissa 21-03-2023 3 1   Download

This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds.

16p vinarcissa 21-03-2023 5 1   Download

VKORC1 has been identified some years ago as the gene encoding vitamin K epoxide reductase (VKOR) – the target protein for coumarin derivates like warfarin or phenprocoumon. Resistance against warfarin and other coumarin-type anticoagulants has been frequently reported over the last 50 years in rodents due to problems in pest control as well as in thrombophilic patients showing variable response to anticoagulant treatment.

7p vinarcissa 21-03-2023 6 1   Download

The QSPR modeling is popularly used in many fields as in silico approach for predicting properties of chemical compounds based on the relationships between the structural characteristics and the properties.

11p viargus 03-03-2023 2 2   Download

Master's thesis of Science "Investigation into the modulation of circadian clock proteins by dietary compounds and small molecules" is structured as follows: Chapter 1 Introduction; Chapter 2 Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNetTM library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity; Chapter 3 Modulation of circadian core clock proteins by dietary compounds; Chapter 4 Molecular mechanisms of action of selected olive phenolics against epigenetic modifiers and the structur...

235p runthenight04 02-02-2023 2 2   Download

Cyclic nucleotide-gated channels (CNGCs) are ligand-gated calcium signaling channels, play vital biological functions. Nonetheless, the CNGC gene families have not been well studied in Brassicaceae which includes commercially important and evolutionary model crops. Here, using in silico approaches, we recognized 414 CNGC genes in sixteen sequenced genomes of Brassicaceae species, which represent 10 genera of 8 tribes, ranging between 10‒51 genes.

53p lyhuyenthu 31-01-2023 8 2   Download

We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle.

13p viaristotle 29-01-2022 9 0   Download

Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data.

20p viarchimedes 26-01-2022 15 0   Download

Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs.

14p viarchimedes 26-01-2022 4 0   Download

Since benzo [b] thiophene scaffold is one of the privileged structures in drug discovery as this core exhibitsactivities for different biological problems, in this study bis (benzo[ b ]thiophene-2-yl) alkyl methanimine derivatives (1-9) were synthesized by reacting benzo[b]thiophene-2-carbaldehyde with diamines. All newly compounds were characterized by IR, 1H NMR and 13C NMR spectroscopic methods.

26p tudichquannguyet 29-11-2021 6 1   Download

The selectivity and the thermostability of EndoBI-1 and EndoBI-2 suggest that these enzymes may be useful for many scientific and industrial applications. In this study, the growing numbers of homologous sequences in different databases were exploited in a comparative approach to investigate structural properties of EndoBI-1 and EndoBI-2 enzymes. Moreover, the complete and partial homology models of these two enzymes were generated and evaluated.

13p tudichquannguyet 29-11-2021 8 2   Download

The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed.

11p thiencuuchu 27-11-2021 11 2   Download

The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome.

14p vibeauty 23-10-2021 10 1   Download

Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and depth of coverage, which is crucial for a successful outcome.

12p vigiselle2711 30-08-2021 16 1   Download

Structural homology modeling supported by bioinformatics analysis plays a key role in uncovering new molecular interactions within gene regulatory networks. Here, we have applied this powerful approach to analyze the molecular interactions orchestrating death receptor signaling networks.

12p visilicon2711 20-08-2021 16 1   Download

The mechanisms of action and efficacy of cisplatin and paclitaxel at cell population level are well studied and documented, however the localized spatio-temporal effects of the drugs are less well understood. We explore the emergence of spatially preferential drug efficacy resulting from variations in mechanisms of cell-drug interactions.

16p vichaeng2711 29-04-2021 9 1   Download